1. Statistical Parametric Mapping
Lecture 5 - Chapter 6
Selection of the optimal pulse sequence for fMRI
Textbook: Functional MRI an introduction to methods, Peter Jezzard, Paul Matthews, and Stephen Smith
Many thanks to those that share their MRI slides online

2. Advantages
Disadvantages
BOLD
Highest activation contrast 2x-4x over perfusion
complicated non-quantitative signal
easiest to implement
no baseline information
multislice trivial
susceptibility artifacts
can use very short TR
Perfusion
unique and quantitative information
low activation contrast
baseline information
longer TR required
easy control over observed vasculature
multislice is difficult
non-invasive
slow mapping of baseline information
no susceptibility artifacts
Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

3. Advantages
Disadvantages
Volume
unique information
invasive
baseline information
susceptibility artifacts
multislice trivial
requires separate run for each task
rapid mapping of baseline information
CMRO2
unique and quantitative information
semi-invasive
extremely low activation contrast
processing intensive
multislice is difficult
longer TR required
Table 6.1b. Continued summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

4. Time/secs 1 2 4 3 Perfusion TI ASL3
Perfusion
Venous outflow
Venous outflow No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins TI
ASL
Figure 6.1a Signal is detected from water spins in the arterial-capillary region of the vasculature and from water in tissues surrounding the capillaries. Relative sensitivity controlled by adjusting TI and by incorporating velocity nulling gradients (also known as diffusion weighting). Nulling and TI~1 sec makes ASL sensitive to capillaries and surrounds.

5. Time/secs 1 2 4 3
Arterial inflow
(BOLD TR < 500 ms)
GE-BOLD No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins
Figure 6.1b Gradient Echo BOLD is sensitive to susceptibility perturbers of all sizes, and are therefore sensitive to all intravasculature and extravascular effects in the capillary-venous portions of the vasculature. If a very short TR is used may show signal from arterial inflow, which can be removed by using a longer TR and/or outer volume saturation.

6. Time/secs 1 2 4 3
Arterial inflow
(BOLD TR < 500 ms)
SE-BOLD No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins
Figure 6.1c Spin Echo BOLD is sensitive to susceptibility perturbers about the size of a red blood cell or capillary, making it predominantly sensitive to intravascular water spins in vessels of all sizes and to extravascular (tissue) water surrounding capillaries. Velocity nulling reduces the signals from larger vessesl.

7. Gradient-echo RF Gx Gz Gy
90° TE
ASL
pulse TI
Spin-echo
180° TE RF Gx Gz Gy
ASL
pulse TI
90°
spin-echo
180° TE RF Gx Gz Gy
90° t
t/2
Figure 6.2 Pulse sequence diagrams of (a) gradient echo, (b) spin echo, and (c) asymmetric spin echo EPI. The TE is shown at the center of 9-line k-space (typically 64 or more lines).  is the offset from center of k-space to echo. Additional pulses needed for ASL are indicated schematically.

8. Approximate GM Relaxation And Activation Induced Rexalation Rate Changes
100 ms
80 ms
T2*
60 ms
50 ms
T2’
150 ms
133.3 ms
DR2 = D(1/T2)
-0.2 s-1
-0.4 s-1
DR2* = D(1/T2*)
-0.8 s-1
-1.6 s-1
DR2’ = D(1/T2’)
-0.6 s-1
-1.2 s-1
T2, T2* and T2’ (from ASE) of GM decrease with increasing field strength
During activation relaxation rates decrease (T2 increase) slightly
Activation induced changes in relaxation rates (R2s) indicate potential for signal production

9. Asymmetric Gradient - echo spin - echo 3 T 1.5 T MRI signal TE (ms) t
0.2
0.4
0.6
0.8 1
-80
-40 40 80
MRI signal
(ms) 70 90
110
130
Spin-echo time (ms) t
3 T
1.5 T
-20 20 60
100
TE (ms)
Gradient - echo
Asymmetric
spin - echo
Figure 6.3a Signal intensity for GE, SE, and ASE for approximate relaxation rates of grey matter at 1.5T and 3T. SE sequence corresponds to ASE at  = 0. Signal decays more rapidly since T2 and T2* is shorter at 3T.

10. Asymmetric Gradient - echo spin - echo Per cent change (ms) t 3 T2 4 6 8 10 12 14 16
-80
-40 40 80
Per cent change
(ms)
130
110 90 70
Spin-echo time (ms) t
3 T
1.5 T 20 60
100
TE (ms)
Gradient - echo
Asymmetric
spin - echo
Figure 6.3b Percent signal change for approximated activation-induced relaxation rate changes (using Table 6.2). Note linear increase for GE and for ASE with |  |>0. Also, 3T shows larger change than 1.5T for all three.

11. Asymmetric Gradient - echo spin - echo Difference (ms) t 3 T 1.5 T
0.01
0.02
0.03
0.04
0.05
-80
-40 40 80
Difference
(ms) 70 90
110
130
Spin-echo time (ms) t
3 T
1.5 T 20 60
100
TE (ms)
Gradient - echo
Asymmetric
spin - echo
Figure 6.3c Signal difference or contrast with brain activation. Peak contrast for GE when TE~T2* and ASE when  ~T2*. SE has lowest contrast.

12. Maximizing Signal Field Strength and sequence parameters RF coils
Higher B means higher SNR but more susceptibility issues
TE ~ T2* ( T) for best activation contrast
TR large enough to cover volume of interest, sampling time consistent with experiment, >500 msec recommended, T1 increases with increasing B
RF coils
Larger coil for transmit
Smaller coil for receive
RF inhomogeneity increases with B
Voxel size
Match to volume of smallest desired functional area
1.5x1.5x1.5 suggested as optimal (Hyde et al., 2000)
T2* increase and activation signal increase with small voxels if shim is poor

13. Maximizing Signal Reducing physiological fluctuations
Cardiac and breathing artifacts (sampling issues)
Filtering to remove artifactual frequencies from time signal, breathing easier to manage by filtering
Pulse sequence strategies
Snap shot (EPI) each image in msec reduces impact of artifacts
Multi-shot ghosting (spiral imaging, navigator pulses, retrospective correction)
Gating
Acquiring image at consistent phase of cardiac cycle or respiration
Problems (changing heart rate, wasted time)

14. Minimizing Temporal Artifacts
Brain activation paradigm timing
On-off cycles usually > 8 seconds
Maximum number of cycles and maximum contrast between
Cycling activations no longer than 3-4 minutes
Post processing
Motion correction
Real time fMRI
Monitoring immediately and repeat if artifacts are excessive
Tuning of slice location

15. Minimizing Temporal Artifacts
Physical restraint
Limited success
Cooperative subject helps
Pulse sequence strategies
Clustered acquisition (auditory stimulation 4-6 seconds before acquisition)
Set phase encode direction to minimize overlap with brain areas of interest
Select image plane with most motion to minimize between plane motion artifacts
Crusher gradients to minimize inflow artifacts

16. Issues of Resolution and Speed
Acquisition speed
Echo planar sequence preferred for fMRI
Multi-shot imaging used for anatomy
Image resolution
Higher resolution takes more time and T2* leads to low signal for later k-space lines
multi-shot EPI
Partial k-space acquisition
Brain Coverage
Full brain coverage desirable
Uniform response throughout brain also needed

17. Structural and Functional Image Quality
Functional time series image quality
Warping
Signal dropout
High resolution structural image quality
3D sub-millimeter possible
Matching functional to structural